Why do the particles in my keyed particle system not hit 2 of the 8 faces of the target mesh?
If I understand keyed particles correctly, they are particles whose position gets interpolated between a start particle of one particle system and a goal particle which belongs to another particle system. I guess something with the matching of the start and the goal particle goes wrong. I guess this is a bug.
To solve this problem, you can disable "Even Distribution" in your goal particle system:


The result looks like it should:


Considering the faces that seem to be unselected in Object mode: If you disable 'Only Render' in the display settings all faces are marked in object mode. Otherwise only the particles are painted in orange, but since the two faces do not get any particles, they don't light up.



Edit: The distribution also works correctly when you set Emit From to "Verts". But then it will only target the vertices of the faces, and that is probably not what you want.